Transcript Catlin: cceHUB as a Research Tool (slides)

cceHUB omicsknowledgebase
An Environment for CCE Research
Ann Christine Catlin
3rd
Annual Cancer Care Engineering Retreat
June 20, 2008
the cancercareengineering model
A systems approach to the prevention and treatment of cancer
1. Patient and Control Blood
Community-based oncology clinics
IUSCC
5. Real-time Visual Analytics
PURVAC, Purdue University
2. Data Acquisition - OMICS,
Prevention, & HSR Data
IUSCC - OMICS Labs
Regenstrief Institute
OMICS Labs, Purdue University
6. Immediate Analysis & Feedback
to Clinics
the CCE Team
3. Data Storage/Query Center
Purdue University
4. Integrative Mathematical
Modeling
Statistics Dept., Purdue University
7. Discovery Research Driven by
Model Predictions
IUSCC
Purdue University
Identify Molecular Signatures for Cancer
How do CCE researchers collaborate?
Mathematical Modeling
OMICs Laboratory
PEG
metabolomics data
LECO GCGCMS
CDF
Visual Analytics
Bio-marker
region
selection
CSV
intensity image viewing
PCA
analysis
TXT
Evaluation of potential bio-markers
Mass spectra navigation
Noise Removal
Comparison
analysis
Statistical analysis
Population-based Modeling
web-based user interface
new viewpoints for input & output
parameter sweep testing
accessibility and usage
educational resources for
community-shared learning
papers, online lectures,
videos, presentations
cceHUB supports CCE research
•
store and backup all OMICS data
•
contribute data from the labs … attach tracking and
search keywords to all datasets
•
explore lab datasets
•
store and backup all modeling tools
•
contribute modeling tools ... shared development
•
run modeling tools in web browser
•
store model results … attach tracking and search
keywords to all results
•
integrate visualization at every step
the cceHUB omicsknowledgebase
immediate & constant availability for
ALL OMICS DATA
ALL MODELING TOOLS
ALL VISUALIZATION TOOLS
promoting the discovery of relationships
end-to-end support for the cceModel
feedback
sample
acquisition
Upload data
Store data
Attach metadata
omics
laboratory
analysis
statistical
modeling
Upload data
Store data
Attach metadata
data
linkage
feedback
predictive
models
integrated
OMICS analysis
visual
analytics
visual
knowledge
discovery
Explore data
feedback
Prepare input
Track model execution
cceHUB
omicsknowledgebase
Store
model results
Attach metadata
What’s at the cceHUB …
Right now …
•
Community-shared
• Educational resources
• Modeling tools
• Data storage & backup
•
User groups, data privacy, modeling tools privacy
•
Help with contributing data and tools
•
Much, much more ...
By September 2008 … Lab Data Uploader, Lab Data Tracking
By September 2009 … Data Explorer, Model Tracking
Data… storage, tracking, exploration
locate data of interest
store & backup
process & store
DATA UPLOADER
DATA EXPLORER
omics omics
omics
omicsdataset
omics
dataset
omics
dataset
omicsdataset
omics
dataset
omics
dataset
omicsdataset
omics
dataset
omics
dataset
omicsdataset
omics
dataset
omics
dataset
omicsdataset
omics
dataset
omics
dataset
dataset dataset
dataset
SHARED DATA REPOSITORY :
omics datasets
Metadata
Database
+
database
Supporting more than OMICS …
OMICS
Knowledge
Base
Health Services
Knowledge
Base
other CCE
Knowledge
Bases
CCE research support
OMICS Knowledge Base
OMICS
Knowledge
Base
Eric Sherer
e-Enterprise Center, VA CoE, IU HSR
Contribute Data & Tools
Store & Backup Data
Explore Data
Run Tools
Track Data & Tools
David Ebert, Wei Chen, Philip Livengood
PURVAC, Purdue University
Dabao Zhang, Min Zhang
Statistics Department, Purdue University
Acknowledgements
• CCE Leadership Team
• Marietta Harrison, Joe Pekny, Julie Nagel
• HUB Development Team
• Mike McLennan, Nick Kisseberg, Swaroop Shivarajapura, George
Howlett, John Rosheck, Derrick Kearney, Rick Kennel, Shawn Rice
• other members of the OMICS Knowledge Base Group
• Seza Orcun, Mourad Ouzzani, Brandi Marshall
• Modeling Groups
• Eric Sherer, Dabao Zhang, Min Zhang
• Visual Analytics Group
• Dave Ebert, Wei Chen, Philip Livengood
Backup Slides
What we need to build …
The cceHUB is built on the HUB cyberinfrastructure, leveraging its modeling and
visualization tools support framework and its community resource-sharing components
create a data support framework
Data Explorer
Metadata-based Query Retrieval
Data Upload
Process Tracking
Results Capture
Data Characterization and Tracking
OMICS Data File Repository
Metadata Database
Data framework: managing end-to-end analysis: data storage, data tracking, data exploration.